BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094105.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 402,328 number of mapped reads = 383,560 (95.34%) number of supplementary alignments = 13,058 (3.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 192,563 number of mapped paired reads (second in pair) = 190,997 number of mapped paired reads (both in pair) = 380,946 number of mapped paired reads (singletons) = 2,614 number of mapped bases = 51,772,458 bp number of sequenced bases = 51,046,695 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 380,365 duplication rate = 47.02% >>>>>>> Insert size mean insert size = 200,864.225 std insert size = 4,357,942.1862 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 31.878 >>>>>>> ACTG content number of A's = 14,483,413 bp (28.37%) number of C's = 11,004,891 bp (21.56%) number of T's = 14,313,727 bp (28.04%) number of G's = 11,243,974 bp (22.03%) number of N's = 690 bp (0%) GC percentage = 43.59% >>>>>>> Mismatches and indels general error rate = 0.0343 number of mismatches = 1,496,309 number of insertions = 60,953 mapped reads with insertion percentage = 15.68% number of deletions = 116,859 mapped reads with deletion percentage = 28.02% homopolymer indels = 28.78% >>>>>>> Coverage mean coverageData = 0.0167X std coverageData = 11.1783X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 394998 0.0015847422903712645 0.8649718143803848 chr2 243199373 2758033 0.011340625454655263 4.9182499167103355 chr3 198022430 1426014 0.0072012751282771355 3.513400449378449 chr4 191154276 1919942 0.010043939587310095 4.222168758095548 chr5 180915260 575182 0.0031792895745776225 1.990816488114585 chr6 171115067 136079 7.952484979011229E-4 0.42811315465543887 chr7 159138663 357289 0.002245142652731725 1.023437756986571 chr8 146364022 1157948 0.007911425117847608 3.967794221829613 chr9 141213431 108184 7.661027653948865E-4 0.27671821904111665 chr10 135534747 390935 0.0028843894916482193 1.3066566831509432 chr11 135006516 2758155 0.020429791699831733 13.283380704421605 chr12 133851895 842767 0.006296264987507274 4.02342924217519 chr13 115169878 3896182 0.03382986999430528 20.570821564021003 chr14 107349540 128761 0.0011994555356268876 0.8315847087940321 chr15 102531392 491007 0.004788845546932592 2.7841981812122882 chr16 90354753 371379 0.004110232031733848 2.909878890506268 chr17 81195210 407897 0.00502365841531785 3.13749413358843 chr18 78077248 653802 0.008373783871070866 5.0157760752683025 chr19 59128983 150941 0.0025527413519018244 0.8357974907409961 chr20 63025520 27590 4.3775918072552197E-4 0.10660638553528126 chr21 48129895 338274 0.007028355245736564 3.614617522178941 chr22 51304566 50410 9.82563618216749E-4 0.2584396012211229 chrMT 16571 13784845 831.8656085933256 3585.3746809785052 chrX 155270560 18435938 0.11873427905457416 20.78291039732487 chrY 59373566 209906 0.0035353443315161498 1.3479735608241405